| stamppAmova {StAMPP} | R Documentation |
Analysis of Molecular Variance
Description
Calculates an AMOVA based on the genetic distance matrix from stamppNeisD() using the amova() function from the package PEGAS for exploring within and between population variation
Usage
stamppAmova(dist.mat, geno, perm = 100)
Arguments
dist.mat |
the matrix of genetic distances between individuals generated from stamppNeisD() |
geno |
a data frame containing allele frequency data generated from stamppConvert, or a genlight object containing genotype data, individual IDs, population IDs and ploidy levels |
perm |
the number of permutations for the tests of hypotheses |
Details
Uses the formula distance ~ populations, to calculate an AMOVA for population differentiation and within & between population variation. This function uses the amova function from the PEGAS package.
Value
An object of class "amova" which is a list containing a table of sum of square deviations (SSD), mean square deviations (MSD) and the number of degrees of freedom as well as the variance components
Author(s)
Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>
References
Paradis E (2010) pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26, 419-420. <doi:10.1093/bioinformatics/btp696>
Examples
# import genotype data and convert to allele frequecies
data(potato.mini, package="StAMPP")
potato.freq <- stamppConvert(potato.mini, "r")
# Calculate genetic distance between individuals
potato.D.ind <- stamppNeisD(potato.freq, FALSE)
# Calculate AMOVA
stamppAmova(potato.D.ind, potato.freq, 100)